Software Updates

Scipion

an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.

RELION

(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

AlphaFold

an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.

ProteinMPNN

is a deep learning based protein sequence design method.

BCFtools

a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

RoseTTAFold

Accurate prediction of protein structures and interactions using a 3-track network

RD Kit

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.

ISOLDE

an immersive environment designed to ease the task of building high quality macromolecular models into low to medium resolution experimental maps, where the experimental information alone is insufficient to place individual atoms precisely. ISOLDE is implemented as a plugin to ChimeraX and can be conveniently installed via its built-in Tool Shed.

SAMtools

(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.

Gnuplot

a portable command-line driven graphing utility originally created to allow scientists and students to visualize mathematical functions and data interactively. It has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like CCP4 and Octave.

ChimeraX

the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.

Rosetta

a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

CCP4

(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.

AlphaFold

an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.

MDAnalysis

an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

AlphaFold

an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.

ChimeraX

the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.

SPHIRE

(SParx for HIgh Resolution Electron microscopy) for cryoEM using statistical resampling to attain quality assessment and result reproducibility. Includes movie frame alignments (movie), CTF estimation of raw electron micrographs (cter), picking/stack creation (window), reproducible 2-D classification (isac), reproducible initial model generation (viper), automatic gold-standard 3-D refinement (meridien), local resolution estimation and filtering (localres), and up to the 3-D sorting of different conformational states based on the statistical 3-D variability of the data (sort3D).